#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
#Copyright 2011. Jason Weirather.
#This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License v3 or any later version.
my $inputfilename = shift @ARGV;
my $outputfilename = shift @ARGV;
my $in  = Bio::AlignIO->new(-file => "$inputfilename" ,
                         -format => 'clustalw');
my $out = Bio::AlignIO->new(-file => ">$outputfilename",
                         -format => 'selex');
while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); }
